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Links from GEO DataSets

Items: 20

1.

Euchromatic chromatin modifications on chromosome 2L

(Submitter supplied) Chromosome-wide analysis of the distribution of H3K4me3, H3K36me2 and H3K36me3 on chromosome 2L. Keywords: ChIP-chip
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL6048
6 Samples
Download data: GPR
Series
Accession:
GSE9414
ID:
200009414
2.

Acetylation on Histone H3 Lysine 9 Mediates a Switch from Transcription Initiation to Elongation

(Submitter supplied) The transition from transcription initiation to elongation is a key regulatory step in gene expression, which requires RNA polymerase II (Pol II) to escape promoter proximal pausing on chromatin. While elongation factors promote pause release leading to transcription elongation, the role of epigenetic modifications during this critical transition step is poorly understood. Two histone marks on histone H3, lysine 4 trimethylation (H3K4me3) and lysine 9 acetylation (H3K9ac), co-localize on active gene promoters and are associated with active transcription. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
5 Samples
Download data: BW
Series
Accession:
GSE99998
ID:
200099998
3.

Depletion of histone deacetylase 3 antagonizes PI3K-mediated tissue overgrowth through the acetylation of histone H4 at lysine 16

(Submitter supplied) Histone acetylation is one of the best studied gene modifications and has been shown to be involved in numerous important biological processes. Herein,we demonstrate that Hdac3 regulates both organ and body size through the deacetylation of histone H4 at lysine 16 (H4K16ac). H4K16ac is affected by PI3K signaling cascades. Increasing H4K16ac by the depletion of Hdac3 counteracts PI3K-induced tissue overgrowth and PI3K-mediated alterations in the transcription profile. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by array
Platform:
GPL1322
4 Samples
Download data: CEL
Series
Accession:
GSE38552
ID:
200038552
4.

Histone H3 K36 trimethylation in wild-type BY4741 yeast strains

(Submitter supplied) ChIP-on chip assays to measure the change in histone H3 K36 trimethylation over the yeast genome in wild-type yeast strains.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by array
Platform:
GPL10930
3 Samples
Download data: TXT
Series
Accession:
GSE37105
ID:
200037105
5.

Sense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

(Submitter supplied) Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL15290
8 Samples
Download data: TXT
Series
Accession:
GSE37102
ID:
200037102
6.

Antisense Cryptic transcription in histone H3 K36A, K56R and K36AK56R mutant yeast strain compared to wild-type

(Submitter supplied) Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in K36A, K56R and K36AK56R mutant yeast strain compared to wildtype.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL15289
8 Samples
Download data: TXT
Series
Accession:
GSE37042
ID:
200037042
7.

Histone H3 K56 acetylation in wild-type histone shuffle strain (YBL574)

(Submitter supplied) ChIP-on chip assays to measure the change in histone H3 K56 acetylation over the yeast genome in wild-type YBL574 yeast strains compared to H3K36A mutant strains.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by array
Platform:
GPL10930
12 Samples
Download data: TXT
Series
Accession:
GSE37039
ID:
200037039
8.

Co-transcriptional histone acetylation is a consequence of histone exchange

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
Platforms:
GPL10930 GPL15289 GPL15290
91 Samples
Download data: TXT
Series
Accession:
GSE28099
ID:
200028099
9.

Histone H4 acetylation in wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains

(Submitter supplied) ChIP-on chip assays to measure the change in histone acetylation over the yeast genome, in ASF1, SET2 and ASF1 SET2 deletion yeast strains compared to the wild-type control. ChIPs of AcH4 from wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains were normalized to the H3 enrichment.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10930
24 Samples
Download data: TXT
Series
Accession:
GSE28098
ID:
200028098
10.

Histone acetylation in wild-type and SET2 deletion yeast strains

(Submitter supplied) ChIP-on chip assays to measure the change in histone acetylation over the yeast genome, in a SET2 deleted strain compared to the wild-type control. ChIPs of H3K9ac, H3K56ac and H4K12ac from wild-type and SET2 deleted cells were normalized to the H3 enrichment.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10930
24 Samples
Download data: TXT
Series
Accession:
GSE28097
ID:
200028097
11.

Histone exchange and histone H4 acetylation in wild-type and SET2 deletion yeast strains

(Submitter supplied) ChIP-on chip assays to measure the change in histone exchange or histone acetylation over the yeast genome, in a SET2 deleted strain compared to the wild-type control. ChIP of Flag and Acetylated H4 from wild-type and SET2 deleted cells were normalized to the Myc enrichment.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10930
18 Samples
Download data: TXT
Series
Accession:
GSE28096
ID:
200028096
12.

A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation

(Submitter supplied) Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. more...
Organism:
Drosophila melanogaster; Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL19057 GPL19132
84 Samples
Download data: BW
Series
Accession:
GSE101646
ID:
200101646
13.

Structural mapping of regulatory function of histone H3 and H4 residues

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL13492 GPL9134
135 Samples
Download data: BED, PAIR, TXT
Series
Accession:
GSE29064
ID:
200029064
14.

Gene expression changes upon the mutation of individual residues of histone H3 and H4

(Submitter supplied) Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL13492
127 Samples
Download data: PAIR, TXT
Series
Accession:
GSE29059
ID:
200029059
15.

Mnase-seq for six histone mutants and two wild-types in S. cerevisiae

(Submitter supplied) Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9134
8 Samples
Download data: BED
Series
Accession:
GSE29026
ID:
200029026
16.

Genomic context-dependent histone H3K36 methylation by Drosophila methyltransferases

(Submitter supplied) How different histone methyltransferases (HMT) cooperate to progressively catalyze different methylation states of the same residue as well the functional consequences of the different methylation states are not well known. Here, we address in the context of Drosophila H3K36 methylation by using single and combinatorial RNAi of HMTs along with genome-wide MNase-ChIPseq analyses. Our study reveals that K36me1/2/3 each mark distinct chromatin compartments. more...
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL33093 GPL19951
107 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE253391
ID:
200253391
17.

Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions

(Submitter supplied) Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21656
30 Samples
Download data: BED
Series
Accession:
GSE125684
ID:
200125684
18.

Intergenerationally maintained Histone H4 lysine 16 acetylation is instructive for future gene activation

(Submitter supplied) Before zygotic genome activation (ZGA) the quiescent genome undergoes reprogramming to transition into the transcriptionally active state. However, the mechanisms underlying euchromatin establishment during early embryogenesis remain poorly understood. Here, we show that histone H4 lysine-16 acetylation (H4K16ac) is maintained from oocytes to fertilized embryos in Drosophila and mammals. H4K16ac forms large domains that control nucleosome accessibility of promoters prior to ZGA in flies. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19132 GPL23323
124 Samples
Download data
Series
Accession:
GSE130335
ID:
200130335
19.

H4K16ac developmental dynamics during Drosophila development [DNA]

(Submitter supplied) H4K16ac developmental dynamics during drosophila development
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL19132 GPL23323
70 Samples
Download data: BED, BEDGRAPH, BW, H5
Series
Accession:
GSE130334
ID:
200130334
20.

H4K16ac developmental dynamics during Drosophila development [RNA]

(Submitter supplied) We have systematically studied the contribution of the histone acetyltransferase MOF for Drosophila embryos development characterizing the expression changes at st5, st7 and st15 in male and female embryos. Additionally, we studied the contribution of the histone acetyltransferase MOF for the transcription of male S2 cells.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23323
54 Samples
Download data: TSV, TXT
Series
Accession:
GSE130333
ID:
200130333
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